stjude/proteinpaint
Nov 2024 – Oct 2025
12 Months active
Languages Used
JavaScriptTextTypeScriptPythontext
Technical Skills
API IntegrationBackend DevelopmentData VisualizationDebuggingDocumentationFront End Development
congyu-lu
PROFILE
Congyu-lu
Over the past year, Chunlei Liu developed and maintained advanced data visualization and analysis features for the stjude/proteinpaint repository, focusing on gene expression, clustering, and cohort-aware workflows. He engineered robust UI components and backend logic using JavaScript, TypeScript, and D3.js, enabling interactive matrix plots, hierarchical clustering, and survival analyses. His work included refactoring API integrations, improving error handling, and standardizing data normalization pipelines to ensure data integrity and reproducibility. By addressing complex edge cases and enhancing release management, Chunlei delivered reliable, maintainable solutions that improved user experience and analytical accuracy for researchers working with large-scale biological datasets.
Overall Statistics
Feature vs Bugs
56%Features
Repository Contributions
149Total
Bugs
36
Commits
149
Features
45
Lines of code
4,090
Activity Months12
Your Network
25 people
Work History
October 2025
6 Commits • 2 Features
Oct 1, 2025Monthly summary for 2025-10 (stjude/proteinpaint): Delivered significant enhancements and stability improvements focused on data accuracy, user control, and backward compatibility. Key outcomes include fixes to group filters UI and data calculations, introduction of a CPM-based filter for volcano plots, and enhanced survival plot time unit support with backward compatibility for older sessions. These changes improve data reliability for researchers, enable more precise analyses, and reduce disruption for existing workflows.
6 Commits • 2 Features
Oct 1, 2025Monthly summary for 2025-10 (stjude/proteinpaint): Delivered significant enhancements and stability improvements focused on data accuracy, user control, and backward compatibility. Key outcomes include fixes to group filters UI and data calculations, introduction of a CPM-based filter for volcano plots, and enhanced survival plot time unit support with backward compatibility for older sessions. These changes improve data reliability for researchers, enable more precise analyses, and reduce disruption for existing workflows.
October 2025
September 2025
21 Commits • 8 Features
Sep 1, 2025September 2025: Delivered substantive improvements to HierCluster workflows, dictionary-term architecture, and UI/performance for the ProteinPaint project, enabling deeper DEG analysis, more reliable term-based clustering, and a smoother user experience. Implemented root-term support for customVariables, global filtering across custom variables, and UI enhancements for gene lists and matrices. Fixed several high-impact bugs to stabilize workflows, improved release documentation, and introduced performance-oriented filtering to scale gene selections.
September 2025
21 Commits • 8 Features
Sep 1, 2025September 2025: Delivered substantive improvements to HierCluster workflows, dictionary-term architecture, and UI/performance for the ProteinPaint project, enabling deeper DEG analysis, more reliable term-based clustering, and a smoother user experience. Implemented root-term support for customVariables, global filtering across custom variables, and UI enhancements for gene lists and matrices. Fixed several high-impact bugs to stabilize workflows, improved release documentation, and introduced performance-oriented filtering to scale gene selections.
August 2025
5 Commits • 2 Features
Aug 1, 2025Concise monthly summary for 2025-08 focusing on business value and technical achievements for stjude/proteinpaint. Highlights include delivered hierarchical clustering color customization, improved SVG legend behavior, and targeted bug fixes that stabilize authentication flow and remove dead code. This month demonstrated strong refactoring, release-note discipline, and code quality improvements that reduce maintenance overhead and improve user experience for clustering workflows.
5 Commits • 2 Features
Aug 1, 2025Concise monthly summary for 2025-08 focusing on business value and technical achievements for stjude/proteinpaint. Highlights include delivered hierarchical clustering color customization, improved SVG legend behavior, and targeted bug fixes that stabilize authentication flow and remove dead code. This month demonstrated strong refactoring, release-note discipline, and code quality improvements that reduce maintenance overhead and improve user experience for clustering workflows.
August 2025
July 2025
8 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for stjude/proteinpaint: Delivered a major feature upgrade for Gene Set Editing UI across clustering views, improved data visualization robustness, and fixed critical data handling issues. Key features delivered: Gene Set Editing UI Revamp in Clustering: consolidated and extended gene set editing UI across hierarchical clustering and genomic alteration charts; renamed panel to '* Clustered Genes'; integrated editing for clustered/unclustered gene sets; standardized button labels to 'N Genes'; updated UI labels and release notes for clarity. Major bugs fixed: Survival Plot Missing Data Handling: introduced a 'Missing data' group to gracefully handle incomplete data and prevent crash/overlay errors; getSampleType Type Conversion Bug: fixed type mismatch by converting sampleId to numeric type before using it as a key to ds.sampleId2Type; Bedgraph Plot Y-Axis Scaling Bug: corrected Y-axis scaling by ensuring fixminv and fixmaxv are used to define the vertical range. Overall impact: more reliable visualizations and editing workflows, reduced user confusion, and clearer product documentation, enabling faster, data-driven decisions. Technologies/skills demonstrated: frontend UI/UX consolidation, defensive data type handling, robust data visualization logic, release-note discipline, and cross-functional collaboration.
July 2025
8 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for stjude/proteinpaint: Delivered a major feature upgrade for Gene Set Editing UI across clustering views, improved data visualization robustness, and fixed critical data handling issues. Key features delivered: Gene Set Editing UI Revamp in Clustering: consolidated and extended gene set editing UI across hierarchical clustering and genomic alteration charts; renamed panel to '* Clustered Genes'; integrated editing for clustered/unclustered gene sets; standardized button labels to 'N Genes'; updated UI labels and release notes for clarity. Major bugs fixed: Survival Plot Missing Data Handling: introduced a 'Missing data' group to gracefully handle incomplete data and prevent crash/overlay errors; getSampleType Type Conversion Bug: fixed type mismatch by converting sampleId to numeric type before using it as a key to ds.sampleId2Type; Bedgraph Plot Y-Axis Scaling Bug: corrected Y-axis scaling by ensuring fixminv and fixmaxv are used to define the vertical range. Overall impact: more reliable visualizations and editing workflows, reduced user confusion, and clearer product documentation, enabling faster, data-driven decisions. Technologies/skills demonstrated: frontend UI/UX consolidation, defensive data type handling, robust data visualization logic, release-note discipline, and cross-functional collaboration.
June 2025
5 Commits • 1 Features
Jun 1, 2025June 2025 monthly summary for stjude/proteinpaint: Delivered targeted data access improvements and UI reliability enhancements that boost data accuracy, user productivity, and maintainability. Implemented get()-based access for GDC assay availability data retrieval with consolidated filtering, and fixed a critical UI option visibility in OncoMatrix gene sets, reducing user friction and support load.
5 Commits • 1 Features
Jun 1, 2025June 2025 monthly summary for stjude/proteinpaint: Delivered targeted data access improvements and UI reliability enhancements that boost data accuracy, user productivity, and maintainability. Implemented get()-based access for GDC assay availability data retrieval with consolidated filtering, and fixed a critical UI option visibility in OncoMatrix gene sets, reducing user friction and support load.
June 2025
May 2025
11 Commits • 2 Features
May 1, 2025May 2025 monthly summary for stjude/proteinpaint. Delivered significant CNV filtering improvements, DTSV support in oncoprint mode, and a robust gene term initialization refactor. These changes collectively enhance data accuracy, visualization fidelity, and maintainability, delivering clear business value to users interpreting gene variants. Key outcomes: - CNV filtering and legend-based criteria enhancements: interactive CNV filtering driven by legend cutoffs, consolidated CNV cutoff configuration, and improved consistency/flexibility of CNV filtering across matrix plots. - DTSV data type support in oncoprint mode: added display support ensuring DTSV values render as tall bars when encoding is single and CNV is not displayed, improving data readability for DTSV datasets. - Refactor of gene term initialization (fillTermWrapper): robust handling of missing IDs and improved data loading, reducing initialization errors and improving startup reliability. - Quality and stability improvements: addressed test failures and legend alignment issues in CNV components, contributing to more reliable releases. Overall impact: - Enhanced data accuracy and user confidence in CNV interpretation and oncoprint visualizations. - Faster iteration and lower maintenance burden through refactors and better configuration management. - Demonstrated proficiency in frontend data visualization, data pipelines, and test maintenance.
May 2025
11 Commits • 2 Features
May 1, 2025May 2025 monthly summary for stjude/proteinpaint. Delivered significant CNV filtering improvements, DTSV support in oncoprint mode, and a robust gene term initialization refactor. These changes collectively enhance data accuracy, visualization fidelity, and maintainability, delivering clear business value to users interpreting gene variants. Key outcomes: - CNV filtering and legend-based criteria enhancements: interactive CNV filtering driven by legend cutoffs, consolidated CNV cutoff configuration, and improved consistency/flexibility of CNV filtering across matrix plots. - DTSV data type support in oncoprint mode: added display support ensuring DTSV values render as tall bars when encoding is single and CNV is not displayed, improving data readability for DTSV datasets. - Refactor of gene term initialization (fillTermWrapper): robust handling of missing IDs and improved data loading, reducing initialization errors and improving startup reliability. - Quality and stability improvements: addressed test failures and legend alignment issues in CNV components, contributing to more reliable releases. Overall impact: - Enhanced data accuracy and user confidence in CNV interpretation and oncoprint visualizations. - Faster iteration and lower maintenance burden through refactors and better configuration management. - Demonstrated proficiency in frontend data visualization, data pipelines, and test maintenance.
April 2025
2 Commits
Apr 1, 2025April 2025: Delivered a critical UI/UX bug fix in gene set loading for hierCluster workflows in stjude/proteinpaint. Removed the 'Load Gene Sets' option from the unclustered genes panel to prevent incorrect loading and to align UI with the intended workflow. Release notes updated to document the fix. Commits related: 11f791b7737521ad2f4977b22b69effed247b892; caf906c2591bd810bac7cd3c9f8251b52a912702.
2 Commits
Apr 1, 2025April 2025: Delivered a critical UI/UX bug fix in gene set loading for hierCluster workflows in stjude/proteinpaint. Removed the 'Load Gene Sets' option from the unclustered genes panel to prevent incorrect loading and to align UI with the intended workflow. Release notes updated to document the fix. Commits related: 11f791b7737521ad2f4977b22b69effed247b892; caf906c2591bd810bac7cd3c9f8251b52a912702.
April 2025
March 2025
24 Commits • 10 Features
Mar 1, 2025March 2025 (Batch 2025-03) — Performance review snapshot for stjude/proteinpaint. Delivered a set of features, fixes, and stability improvements that expand analytical capabilities, improve data fidelity, and streamline user workflows. Key technical and business-value outcomes include enabling DE analysis for a single-group custom term, enriching visual analytics with violin plots across custom terms and numeric term types, and executing UI/UX enhancements that simplify cluster management and terms navigation. Also standardized data normalization, strengthened API reliability, and documented batch releases to improve cross-team communication and release traceability. Key feature deliveries: - Enabled differential expression (DE) analysis for a custom term when only a single group is present (commit 025181a5386c59ae6f1e05f0f349813901da239c). - Added violin plot visualizations for gene expression summarization: for a custom term (commit 289451efaa7af539f761a54e27de29cce234d570) and for all numeric term types (commit adf49488403aefe0f9e44a7d04cf824d6b871d3f). - UI/UX enhancements in HierCluster and related panels, including cluster/unCluster checkboxes, sorting options for terms within hierCluster groups, and Genes panel rename/UI tweaks (commits 4e49ee97dc3422d3711d244d6a778f4992cf79a2; 33c656b014ca0ac9afb2bc96983212076b45b678; ea8e4b05550c20d7cbf3f7ddb62c4fa1400408b9). - Uniform Z-score normalization applied across the data processing pipeline (commit ecf2dfd529319b780830d9d84aefc7193d2d9ec6). - Release management and API hygiene: Batch 2025-03 release notes and API typings updates to reflect current API usage (commits fd81853e1e51608fc8dab5a01dc2f5ce02eea4c4; f0e31378e6d4ac561855a6ee2c5786da6c9b0bd2; 2edb6314102b6f466f9049f7ca44fefb7f0f8a30). Major bug fixes: - Corrected sample size calculation for the 'other' group when it is 0 and when global filters are applied (commits cc7227acbb46ea808d00b3ac9d49a46d8cfbfa94; 0994fdab039ec5c8f1dd36e90db4cf38ffc4e831). - Backend messaging: ensure clients are informed when gene/terms in the request body are skipped by the backend (commit a296a2996ddf5bc91e6a3bc49691465f11bd740b). - Treat removal of terms as an error condition to prevent silent data inconsistencies (commit 222c00d7d7622fd0eb4f63ad8d383c66f6536e50). - Update ValidResponse type to reflect current API (commit 2edb6314102b6f466f9049f7ca44fefb7f0f8a30). - Convert numeric labels to strings to avoid type inconsistencies (commit b1fd4b190c696c83f37f51cb2f58c8a9d9198d24). - Fix color change bug in barchart legend (commit dd49ac8772b6d971dc78b41f17653e5d4f2fac74). - Miscellaneous polish: typo fixes (commit 70e51bda4d30291d30e7f1ccefdfe7512505dcd9); navigation fix back to Genes panel (commit c2469fdda332dbf8338f93bbe4d8e02d36f79435). Overall impact and accomplishments: - Expanded analytical capabilities while maintaining data integrity and stability across the platform. - Improved interpretability of results via violin plots and consistent normalization. - Streamlined workflows through HierCluster/UI enhancements and smoother navigation. - Strengthened release discipline and API consistency to support faster, more reliable deployments. Technologies and skills demonstrated: - Frontend visualization and UI/UX improvements, TypeScript/JavaScript, data visualization (violin plots, barcharts), and responsive design patterns. - Data processing and normalization (Z-score normalization) across pipelines. - API design and error handling improvements, including ValidResponse alignment and backend-to-client messaging. - Release engineering, documentation, and cross-team communication.
March 2025
24 Commits • 10 Features
Mar 1, 2025March 2025 (Batch 2025-03) — Performance review snapshot for stjude/proteinpaint. Delivered a set of features, fixes, and stability improvements that expand analytical capabilities, improve data fidelity, and streamline user workflows. Key technical and business-value outcomes include enabling DE analysis for a single-group custom term, enriching visual analytics with violin plots across custom terms and numeric term types, and executing UI/UX enhancements that simplify cluster management and terms navigation. Also standardized data normalization, strengthened API reliability, and documented batch releases to improve cross-team communication and release traceability. Key feature deliveries: - Enabled differential expression (DE) analysis for a custom term when only a single group is present (commit 025181a5386c59ae6f1e05f0f349813901da239c). - Added violin plot visualizations for gene expression summarization: for a custom term (commit 289451efaa7af539f761a54e27de29cce234d570) and for all numeric term types (commit adf49488403aefe0f9e44a7d04cf824d6b871d3f). - UI/UX enhancements in HierCluster and related panels, including cluster/unCluster checkboxes, sorting options for terms within hierCluster groups, and Genes panel rename/UI tweaks (commits 4e49ee97dc3422d3711d244d6a778f4992cf79a2; 33c656b014ca0ac9afb2bc96983212076b45b678; ea8e4b05550c20d7cbf3f7ddb62c4fa1400408b9). - Uniform Z-score normalization applied across the data processing pipeline (commit ecf2dfd529319b780830d9d84aefc7193d2d9ec6). - Release management and API hygiene: Batch 2025-03 release notes and API typings updates to reflect current API usage (commits fd81853e1e51608fc8dab5a01dc2f5ce02eea4c4; f0e31378e6d4ac561855a6ee2c5786da6c9b0bd2; 2edb6314102b6f466f9049f7ca44fefb7f0f8a30). Major bug fixes: - Corrected sample size calculation for the 'other' group when it is 0 and when global filters are applied (commits cc7227acbb46ea808d00b3ac9d49a46d8cfbfa94; 0994fdab039ec5c8f1dd36e90db4cf38ffc4e831). - Backend messaging: ensure clients are informed when gene/terms in the request body are skipped by the backend (commit a296a2996ddf5bc91e6a3bc49691465f11bd740b). - Treat removal of terms as an error condition to prevent silent data inconsistencies (commit 222c00d7d7622fd0eb4f63ad8d383c66f6536e50). - Update ValidResponse type to reflect current API (commit 2edb6314102b6f466f9049f7ca44fefb7f0f8a30). - Convert numeric labels to strings to avoid type inconsistencies (commit b1fd4b190c696c83f37f51cb2f58c8a9d9198d24). - Fix color change bug in barchart legend (commit dd49ac8772b6d971dc78b41f17653e5d4f2fac74). - Miscellaneous polish: typo fixes (commit 70e51bda4d30291d30e7f1ccefdfe7512505dcd9); navigation fix back to Genes panel (commit c2469fdda332dbf8338f93bbe4d8e02d36f79435). Overall impact and accomplishments: - Expanded analytical capabilities while maintaining data integrity and stability across the platform. - Improved interpretability of results via violin plots and consistent normalization. - Streamlined workflows through HierCluster/UI enhancements and smoother navigation. - Strengthened release discipline and API consistency to support faster, more reliable deployments. Technologies and skills demonstrated: - Frontend visualization and UI/UX improvements, TypeScript/JavaScript, data visualization (violin plots, barcharts), and responsive design patterns. - Data processing and normalization (Z-score normalization) across pipelines. - API design and error handling improvements, including ValidResponse alignment and backend-to-client messaging. - Release engineering, documentation, and cross-team communication.
February 2025
6 Commits • 2 Features
Feb 1, 2025February 2025 performance summary for stjude/proteinpaint. Delivered critical enhancements to clustering reliability and data integrity across multiple data sources, along with visualization stability improvements, resulting in more robust analyses and a smoother user experience. Focused on reducing downstream errors, improving reproducibility, and ensuring consistent visuals across datasets.
6 Commits • 2 Features
Feb 1, 2025February 2025 performance summary for stjude/proteinpaint. Delivered critical enhancements to clustering reliability and data integrity across multiple data sources, along with visualization stability improvements, resulting in more robust analyses and a smoother user experience. Focused on reducing downstream errors, improving reproducibility, and ensuring consistent visuals across datasets.
February 2025
January 2025
30 Commits • 11 Features
Jan 1, 2025January 2025 monthly summary for stjude/proteinpaint. Focused on delivering cohort-aware UI improvements, expanding plotting capabilities, fixing stability issues, and improving maintainability to drive accurate data analysis and faster workflows for users analyzing across cohorts.
January 2025
30 Commits • 11 Features
Jan 1, 2025January 2025 monthly summary for stjude/proteinpaint. Focused on delivering cohort-aware UI improvements, expanding plotting capabilities, fixing stability issues, and improving maintainability to drive accurate data analysis and faster workflows for users analyzing across cohorts.
December 2024
20 Commits • 4 Features
Dec 1, 2024December 2024 monthly summary for stjude/proteinpaint: Delivered robust visualization enhancements across matrix, barchart, brain imaging, and CNV modules, along with stability fixes to improve data exploration and user experience. Key features delivered included Matrix Visualization Enhancements (per-term settings, legend colors, improved color scales), removal of text input option, and TypeScript robustness; Barchart: Multiple Testing Correction toggle with MTC method labeling; Brain Imaging Visualization Improvements (geneVariant terms, color handling, division/overlay capabilities, removal of redundant script); CNV Classification and 5-Category CNV with ordered display and updated GDC support; Single-Cell Plot Reliability and UX Fixes with improved error handling and UI messaging. Major bugs fixed include improved single-cell error display, resolution of TypeScript errors, and removal of a duplicate brain Imaging script. Release notes accompany all changes to document user impact. Overall impact: enhanced data exploration, more accurate and consistent visualizations, reduced user errors, and stronger platform stability, enabling faster, data-driven decisions. Technologies/skills demonstrated: TypeScript robustness, UI/UX improvements, release-note discipline, error handling, dictionary-tree UI interactions, and advanced color scale management.
20 Commits • 4 Features
Dec 1, 2024December 2024 monthly summary for stjude/proteinpaint: Delivered robust visualization enhancements across matrix, barchart, brain imaging, and CNV modules, along with stability fixes to improve data exploration and user experience. Key features delivered included Matrix Visualization Enhancements (per-term settings, legend colors, improved color scales), removal of text input option, and TypeScript robustness; Barchart: Multiple Testing Correction toggle with MTC method labeling; Brain Imaging Visualization Improvements (geneVariant terms, color handling, division/overlay capabilities, removal of redundant script); CNV Classification and 5-Category CNV with ordered display and updated GDC support; Single-Cell Plot Reliability and UX Fixes with improved error handling and UI messaging. Major bugs fixed include improved single-cell error display, resolution of TypeScript errors, and removal of a duplicate brain Imaging script. Release notes accompany all changes to document user impact. Overall impact: enhanced data exploration, more accurate and consistent visualizations, reduced user errors, and stronger platform stability, enabling faster, data-driven decisions. Technologies/skills demonstrated: TypeScript robustness, UI/UX improvements, release-note discipline, error handling, dictionary-tree UI interactions, and advanced color scale management.
December 2024
November 2024
11 Commits • 2 Features
Nov 1, 2024November 2024 monthly summary for stjude/proteinpaint: Delivered plotting enhancements, stability improvements, and groundwork for API consistency. Implemented matrix continuous plot customization with user-configurable row height and bar color and UI label editing; enabled robust matrix/term handling to allow launching matrix/hiercluster plots from custom terms; ensured 0 values are visible in tooltips and click menus for matrix/hiercluster plots; added a destroy method to fix matrix resize errors after sandbox cross-out; enabled 95% confidence interval by default in survival plots. This cycle also included internal maintenance tasks to pave the way for API settings consistency and improved documentation.
November 2024
11 Commits • 2 Features
Nov 1, 2024November 2024 monthly summary for stjude/proteinpaint: Delivered plotting enhancements, stability improvements, and groundwork for API consistency. Implemented matrix continuous plot customization with user-configurable row height and bar color and UI label editing; enabled robust matrix/term handling to allow launching matrix/hiercluster plots from custom terms; ensured 0 values are visible in tooltips and click menus for matrix/hiercluster plots; added a destroy method to fix matrix resize errors after sandbox cross-out; enabled 95% confidence interval by default in survival plots. This cycle also included internal maintenance tasks to pave the way for API settings consistency and improved documentation.
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Quality Metrics
Correctness87.4%
Maintainability87.8%
Architecture81.8%
Performance80.8%
AI Usage20.2%
Skills & Technologies
Programming Languages
JavaScriptPythonTextTypeScripttext
Technical Skills
API DevelopmentAPI IntegrationAPI RefactoringAlgorithm ImplementationAuthenticationBack End DevelopmentBackend DevelopmentBug FixingCode DocumentationCode RefactoringConfiguration ManagementD3.jsData AnalysisData FilteringData Handling
Repositories Contributed To
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